Data Quality Assessment Report

massqc from tidymass by Xiaotao Shen

2024-12-31

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INTRODUCTION

massqc (version 0.01): Created in 2021 by Xiaotao Shen

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PARAMETERS

Table 1: Parameter setting

pacakge_name	function_name	parameter	time
massprocesser	process_data	path:/home/data/shawn/02.project/33.cyk/seedling/working_dir/02.progress/transform/MS1/POS/	2024-12-31 10:51:32
massprocesser	process_data	polarity:positive	2024-12-31 10:51:32
massprocesser	process_data	ppm:8	2024-12-31 10:51:32
massprocesser	process_data	peakwidth:5,25	2024-12-31 10:51:32
massprocesser	process_data	snthresh:3	2024-12-31 10:51:32
massprocesser	process_data	prefilter:3,11460	2024-12-31 10:51:32
massprocesser	process_data	fitgauss:FALSE	2024-12-31 10:51:32
massprocesser	process_data	integrate:1	2024-12-31 10:51:32
massprocesser	process_data	mzdiff:-0.01	2024-12-31 10:51:32
massprocesser	process_data	noise:11460	2024-12-31 10:51:32
massprocesser	process_data	threads:40	2024-12-31 10:51:32
massprocesser	process_data	binSize:0.025	2024-12-31 10:51:32
massprocesser	process_data	bw:5	2024-12-31 10:51:32
massprocesser	process_data	output_tic:TRUE	2024-12-31 10:51:32
massprocesser	process_data	output_bpc:TRUE	2024-12-31 10:51:32
massprocesser	process_data	output_rt_correction_plot:TRUE	2024-12-31 10:51:32
massprocesser	process_data	min_fraction:0.5	2024-12-31 10:51:32
massprocesser	process_data	fill_peaks:FALSE	2024-12-31 10:51:32
massdataset	create_mass_dataset()	no:no	2024-12-31 10:53:20

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SAMPLE INFORMATION

#> -------------------- 
#> massdataset version: 1.0.5 
#> -------------------- 
#> 1.expression_data:[ 6314 x 22 data.frame]
#> 2.sample_info:[ 22 x 5 data.frame]
#> 3.variable_info:[ 6314 x 3 data.frame]
#> 4.sample_info_note:[ 5 x 2 data.frame]
#> 5.variable_info_note:[ 3 x 2 data.frame]
#> 6.ms2_data:[ 0 variables x 0 MS2 spectra]
#> -------------------- 
#> Processing information (extract_process_info())
#> create_mass_dataset ---------- 
#>       Package         Function.used                Time
#> 1 massdataset create_mass_dataset() 2024-12-31 10:53:20
#> process_data ---------- 
#>         Package Function.used                Time
#> 1 massprocesser  process_data 2024-12-31 10:51:32

Figure 1: Peak intensity profile.

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MISSING VALUES

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MISSING VALUES IN DATASET

Black is MV.

Figure 2: Missing values in dataset

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MISSING VALUES IN VARIABLES

Figure 3: Missing values in variables

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MISSING VALUES IN SAMPLES

Figure 4: Missing values in samples

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RSD DISTRIBUTATION

Figure 5: RSD distributation

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INTENSITY FOR ALL THE VARIABLES

Figure 6: Intensity for all the variables

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SAMPLE CORRELATION

Figure 7: Sample correlation

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PCA score plot

Figure 7: PCA score plot